OverExpressed

Posts Tagged ‘biology’

I’m about to see some things that can’t be unseen, to learn some things that can’t be unlearned, and to think some things that can’t be unthought. Within less than a fortnight, a significant amount of my genetic destiny will be revealed to me by the magic of consumer genetics. And the suspense is killing me.

As a metrics and diy bio junky, I’ve been very eager to explore the essential blueprints to my being. It’s incredible to even imagine that most everything I am can be reduced to a fundamental set of instructions based on patterns of just four letters (the rest can be accounted for by ‘nurture’, which for me is mainly an amalgam of adventure novels and Saved by the Bell episodes, as best I can tell).

When I first heard about 23andme several years ago, I was pretty sure the future was coming fast. However, the price tag was still a bit steep for me. Considering the Moore’s Law depreciation of sequencing costs, I just couldn’t rationalize the expense for a report that didn’t even cover my entire genome. I even signed up for the Personal Genome Project in the interim. Unfortunately, they still haven’t taken me in, and my enrollment seems unlikely given their preference for people with known rare genetic conditions. So I’ve waited for the price to go down.

Happy DNA Day!

And finally an opportunity for low-cost genotyping! April 23rd was National DNA Day, during which 23andme (named after your 23 chromosome pairs), offered their full package (including ancestry, health, and extended sequence access) for just $99. This was a $400 discount from the normal $499 price tag. Obviously, I jumped on the deal.

Of course, 23andme is just one of many consumer sequencing companies (including Navegenics, deCODEme, and Knome, among others). However, 23andme offers one of the most complete offerings I’ve found. They give you ~600,000 known “single nucleotide polymorphisms” (or SNP’s, basically just single letters in your sequence where you’re likely to vary from others in a meaningful way), including mitochondrial DNA. Granted, this is just a small portion of my entire genome (only ~0.02% of my 3 billion bases, to be ~exact). However, it represents many of the significant places (or loci) where I differ from you or anyone else. It also includes many compelling factors involved with a range of heritable conditions. And I’ll be particularly interested to learn things like my eye and hair color.

Some Reasonable Caution

Now, it’s not a terrible idea to take a step back and consider the consequences of such deep self-knowledge. First of all, I have to ponder the psychological impacts this information could have on me. What if I find out I have some rare genetic disorder that is reliably linked to a terminal illness? What if I find some factors that would indicate the need for a drastic change in lifestyle? What if my dad isn’t my dad? What if I find that I’m completely boring, genetically? These are all possibilities. But I’m prepared (or at least momentarily indifferent) to their consequences. I believe that understanding the root of your medical condition can help you make educated choices moving forward, and I intend to leverage any information I gain.

However, I am slightly more suspicious of the potential legal implications. Just imagine a Gattaca-esque world (by the way – notice the title is made of A, T, G, C) where your job, insurance, and even mate, are essentially determined by the strength of your genetic code. That’s some pretty scary stuff. And most people don’t seem to realize how close we are to this (at least technologically). There are already a number of opportunities for genetic theft. It will be very important for the government to enact some tough regulations that can withstand any assault on personal genomic privacy. Fortunately, we currently have a law protecting us from genetic discrimination with respect to insurance and employment.

What I Hope to Get Out of This

It’s no secret that I’m a fan of data. I’d like to be as quantitative as possible in my life choices. Within the realm of health, this has primarily manifested itself in the use of activity-tracking applicaitons, such as CardioTrainer for running and Daily Burn (formerly Gyminee) for weight training. However, my genome represents a vast bank of data that I could never empirically derive by phenotypic analysis alone. I’m super excited to finally get access to even a small portion of this raw data.

Although obviously I could have accessed a lot of this information by myself using several methods (including outsourcing directly to Illumina, as 23andme has done), I wanted to go through one of these companies (and 23andme in particular). This is mainly because I appreciate all of the additional analysis and formatting they provide in presenting the absolutely daunting amount of information contained in my raw genetic sequences. They’ve developed some simple tools to show my ancestry, as well as my health risks (weighted by the reliability of the associated studies in a 5-star format) in a secure, web-based format. Though I could collect and analyze this information myself, it would certainly take a significant amount of effort, and thus I’m willing to pay a service to provide this convenient user experience.

And speaking of user experience, it’s interesting to note the relationship between 23andme and Google. Specifically, 23andme received a significant amount of funding from Google (mildly controversial since 23andme cofounder Anne Wojcicki is married to Google cofounder Sergey Brin). But this all makes sense to me. It is Google’s stated goal to “organize the world’s information and make it universally accessible and useful.” Personal genomic data is perhaps some of the most useful information out there, and Google clearly has an interest in organizing it. Considering what they’ve done for the web, I’m excited to see what they can do to simplify genetic relationships. And I suppose I’m about to find out. All my base are belong to Google.

It’s the first day of summer, and it’s high time I finally joined the big conversation happening on the internet. Sure, I’ve been participating semi-passively through google reader, facebook, friendfeed, twitter, etc. for a while now. I have alpha and beta accounts with just about every newfangled web service in existence. But now I’d like to pour a little bit of my voice into this shiny new blog. Yes, a blog. I’ve finally caught up with the 90’s. I think I’m ready to tackle some topics that require a little more than 140 characters.

Why Blog?

I’m a big fan of Seth Godin (a popular marketing guru). One of his many nuggets of wisdom that has stuck with me relates to the cost of now. Basically, you pay a high price to get something sooner. For me, I have some sort of unhealthy thirst for information that leads me to be constantly tapped into the next big thing in science & technology. I willingly jam my mouth right in the firehose’s path. And doing this puts me in a unique position to process and assess cutting-edge ideas and technologies. Seth warns that if you pay the price for this information, you should do what you can to leverage it:

Sometimes, in our quest for the new, we overpay. Most of the time, moving down the curve will decrease your costs dramatically, without hurting your ability to make smart decisions. Alternatively, when you choose to spend the time (or money), leverage it like crazy.

Right now I share what I learn with close friends and through a slightly larger network on Google Reader. But now I think it’s time for me to put more of my own ideas in writing. Obviously my primary motivation here is to get some boss street cred, but I also hope to contribute something practical to the lives of my readers. You’re drowning in a sea of science and technology, and I’ll be your lifeboat. Or at least positively buoyant. Like a stick. A floating stick named Rick.

Science, Technology, and Productivity in Bioengineering

So let’s start with some background. I’m a bioengineer. If you don’t know what that is, it’s probably because nobody has really defined it that well yet. It’s a painfully nebulous term that covers everything from genomics to computational biology to prosthetic limb replacement. If it involves biology in any combination with mechanics, chemistry, physics, electrostatics, computer science, or business, people can and have categorized it as “bioengineering”. I specifically place myself in the neat little area of biomolecular phenomena, explored through the lens of micro- and nano-fabricated materials and structures. I basically put things like DNA and proteins in small chambers to try and make some sweet tools for applications like rapid, inexpensive diagnostics.

As a bioengineer you often find yourself at the interface of ologies, ometries, and omicses. It’s all part of the Bio2.0 bubble. Want more funding? Make up a word. Add a convincing suffix and you’re all set. We’re drowning in acronyms and initiatives to the point where nothing means anything anymore. What’s really up with cancer? What about HIV? Why can’t I just clone an extra liver for the weekends? When will I get my genome and what the hell am I going to do with it? Science hasn’t always had the best record when it comes to public relations. Hopefully I can leverage some of my interests and expertise to shine some light in this oftentimes shady expanse.

To improve the science, though, I also believe in the power of working smarter, not harder. This drives me to optimize the tools I use on a daily basis so that I can get more for dime my time (TM). More perk for my work (TM). More spinach for my minutes (TM). More pepper for my effort (TM). Man, I could do this all day. And for this, I apologize. I don’t even know what pepper would be in that analogy.

Back to the point, I currently share these tools with friends and family in a pretty low-throughput manner. But now, with OverExpressed, I’m making a one-stop-shop for all of this information. Hopefully you can find something useful here, and if you have any comments or feedback, you can’t overexpress them enough. Ha.